/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#ifndef BOLSCORINGMODELSHAREDPEAKCOUNT_H
#define BOLSCORINGMODELSHAREDPEAKCOUNT_H

#include <utils/spectraalignmentscoringmodel.h>
#include <utils/peaktheomsms.h>


namespace bol {

/**
count the shared peak bextween two spectra

	@author Alexandre Masselot,GeneBio,http://www.genebio.com, <alexandre.masselot@gmail.com>
*/
  class ScoringModelSharedPeakCount: public SpectraAlignmentScoringModel<PeakTheoMsms, PeakIntensity>{
public:
    /**
     * nothing special at construction time
     */
    ScoringModelSharedPeakCount();

    /**
     * 
     */
    ~ScoringModelSharedPeakCount();

    void init();

    /**
     * count the peak with an alignement
     * @param spalign 
     * @return 
     */
    double score(const SpectraAlignment<PeakTheoMsms, PeakIntensity>& spalign);

    /**
     * there is no learning phase for this scoring!
     */
    void learn_init();
    /**
     * there is no learning phase for this scoring!
     * @param spalign 
     */
    /**
     * there is no learning phase for this scoring!
     * @param spalign 
     */
    void learn_pushAlternate(const SpectraAlignment<PeakTheoMsms,PeakIntensity>& spalign);
    /**
     * there is no learning phase for this scoring!
     * @param spalign 
     */
    /**
     * there is no learning phase for this scoring!
     * @param spalign 
     */
    void learn_pushNull(const SpectraAlignment<PeakTheoMsms,PeakIntensity>& spalign);
    /**
     * there is no learning phase for this scoring!
     */
    void learn_finalize();

};

}

#endif
